Purchased my first skyline about 6 months ago and was very apprehensive as well;
Make sure you get the full vehicle report from qld transport - costs about $30 online and show's registration history/km's, accident history and a rev's certificate. Naturally you want to get as much documentation about the car as possible from the owner, and ensure it all matches up with the VIN/import sticker/engine block stamp (make sure you cite this in person). I got a mechanic mate to come along with me - if you don't have one get a full inspection done, definitely worth the money. You should also test drive more than one, unless you have driven skylines in the past, to get an idea of how the car feels compared to other examples.
In terms of being thrashed, whether the km's are legit etc - its all hard to corroborate. Give aways are adjustable boost controllers, lower tread on the rear tyres compared to the front, tyre rubber stuck on the inner rear guards, heavy steering wheel/handbrake/arm rest wear. I'm sure others on here could give you a lot of other things to look for. Also recommend you check out this guide for a comprehensive check list.
Also, evaluate the individual - I don't like to stereotype but it all adds to painting a clearer picture of the vehicle. How long have they owned the car? genuine reason for sale? what other cars do/have they owned? mature enthusiast or 21y.o flat brimmer?
Last piece of advice is to be patient - if it seems too good to be true it most probably is. You have to be prepared to wait for that honest example to come along, it will be worth the wait. Good luck!